Ecce Perago and Annon certainly treat SCP-666-J as real, though they don't refer to it as such. There's a Resurrection tale that involves a few of the -Js, but IIRC, no numbers for that one either. I can't think of any that do. Unless you count individual tales that take a -J and make it serious, but those don't usually involve any other SCPs.

I was wondering if any author of serious tales has tried to reference joke SCPs as real, and if so how they explained the numbering?

The joke SCPs associated with Kiryu Labs are effectively "real", in that they're actual things that exist in-universe (SCP-3333-J Is Dr. Mercer's potted spider plant, SCP-723-J is a cockroach that lives in the break room, and SCP-732-J is a knickknack on Dr. Kiryu's desk).

Granted, none of those (to my memory anyway, and my memory is admittedly fuzzy) are mentioned explicitly in the Kiryu labs tales, but if they were, they'd probably just be called conversational things like "the plant", "that roach", and "the tiny ceramic seahorse" or the like.